Use tighter version control for python packages on python singu image

python_3.9.def

@@ -31,7 +31,6 @@ dnf install -y epel-release
 dnf update -y libmodulemd
 dnf update -y --exclude=filesystem
 # filesystem packages updates poses problems by tempering with /proc, which is supposed to be owned by root, but is not in the .sif image
-
 dnf remove -y python3 && dnf autoremove
 dnf install -y python39 git-2.27.0-1.el8.x86_64 compat-openssl10.x86_64
 
@@ -40,18 +39,20 @@ git clone --branch ${GAD_VERSION} http://gitlab.gad-bioinfo.org/gad/gadpipeline.
 
 mv -v /data/gadpipeline/common/GeneralTools.py /data/gadpipeline/common/LabkeyTools.py /data/gadpipeline/common/InterTools.py /data/gadpipeline/common/VcfTools.py /data/gadpipeline/common/CnvTools.py /usr/lib/python3.9/site-packages/
 
+printf "labkey==1.4.0\nnumpy==2.0.2\nmatplotlib==3.9.4\npandas==2.2.3\nchart-studio==1.1.0\nscipy==1.13.1\npyvcf==0.6.8\nsimplejson==3.19.3\nmodified-thompson-tau-test==0.1.3\n" > constraints.txt
+
 # install python pip packages
-pip3.9 install --upgrade -t /usr/lib/python3.9/site-packages/ labkey==1.4.0
-pip3.9 install --upgrade -t /usr/lib/python3.9/site-packages/ numpy==2.0.2
-pip3.9 install --upgrade -t /usr/lib/python3.9/site-packages/ matplotlib==3.9.4
-pip3.9 install --upgrade -t /usr/lib/python3.9/site-packages/ pandas==2.2.3
+pip3.9 install --upgrade -t /usr/lib/python3.9/site-packages/ labkey -c constraints.txt
+pip3.9 install --upgrade -t /usr/lib/python3.9/site-packages/ numpy -c constraints.txt
+pip3.9 install --upgrade -t /usr/lib/python3.9/site-packages/ matplotlib -c constraints.txt
+pip3.9 install --upgrade -t /usr/lib/python3.9/site-packages/ pandas -c constraints.txt
 # pip3.9 install --upgrade -t /usr/lib/python3.9/site-packages/ plotly
 # is causing an error due to plotly.plotly module being deprecated in python3.9. chart-studio package (with the chart_studio.plotly module) is to be used in replacement.
-pip3.9 install --upgrade -t /usr/lib/python3.9/site-packages/ chart-studio==1.1.0
-pip3.9 install --upgrade -t /usr/lib/python3.9/site-packages/ scipy==1.13.1
-pip3.9 install --upgrade -t /usr/lib/python3.9/site-packages/ pyvcf==0.6.8
-pip3.9 install --upgrade -t /usr/lib/python3.9/site-packages/ simplejson==3.19.3
-pip3.9 install --upgrade -t /usr/lib/python3.9/site-packages/ modified-thompson-tau-test==0.1.3
+pip3.9 install --upgrade -t /usr/lib/python3.9/site-packages/ chart-studio -c constraints.txt
+pip3.9 install --upgrade -t /usr/lib/python3.9/site-packages/ scipy -c constraints.txt
+pip3.9 install --upgrade -t /usr/lib/python3.9/site-packages/ pyvcf -c constraints.txt
+pip3.9 install --upgrade -t /usr/lib/python3.9/site-packages/ simplejson -c constraints.txt
+pip3.9 install --upgrade -t /usr/lib/python3.9/site-packages/ modified-thompson-tau-test -c constraints.txt
 
 #cleaning
 rm -rf /data/